These methods all estimate divergence times very similar to Zuckerkandl and Pauling's original conception of the molecular clock.
We adopted a standard two-step procedure to estimate divergence times.
To estimate divergence times, we performed phylogenetic analysis on three potentially informative regions, shown in black in Figure 6A.
To estimate divergence times, likelihood ratio test was performed using PAUP*4.0b to obtain the likelihood scores and investigate whether a global clock fit the combined dataset.
The uncorrelated Bayesian model of rate change implemented in BEAST ver. 1.4.4 [13] was used to estimate divergence times and to determine rates.
Maximum likelihood trees (as described above) of each of the five Macaronesian clades were used to estimate divergence dates using Bayesian methods implemented in Multidivtime [57], [58].
Schuenzel et al. [7] used the rate of synonymous substitutions in these subspecific branches to estimate divergence times, and found that the rate in the X. fastidiosa subspp.
The objective of the original study [7] was to estimate divergence times of mouse lemurs (genus: Microcebus), the world's smallest primates, endemic to Madagascar.
A Bayesian-based approach, incorporating multiple fossil calibration points, was used to estimate divergence times for critical nodes in the phylogeny.
For example, Drummond et al. [39] recently developed a set of Bayesian procedures to jointly estimate divergence times, evolutionary rates, and the tree topology.
Samples examined in the study to estimate divergence times.
